Cyanobacteria in microbial mats from Antarctic lakes

Последняя версия опубликована SCAR - Microbial Antarctic Resource System Mar 19, 2019 SCAR - Microbial Antarctic Resource System

Amplicon sequencing dataset targeting Cyanobacteria (16S ssu rRNA gene) in microbial benthic mats from 13 lakes across the Antarctic continent.

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Как оформить ссылку

Исследователи должны дать ссылку на эту работу следующим образом:

Pessi I, Lara Y, Durieu B, de C. Maarouf P, Verleyen E, Wilmotte A (2019): Cyanobacteria in microbial mats from Antarctic lakes. v1.2. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=lacustrine_cyanobacteria_antarctica&v=1.2

Права

Исследователи должны соблюдать следующие права:

Публикующей организацией и владельцем прав на данную работу является SCAR - Microbial Antarctic Resource System. This work is licensed under a Creative Commons Attribution (CC-BY) 4.0 License.

Регистрация в GBIF

Этот ресурс был зарегистрирован в GBIF, ему был присвоен следующий UUID: a41ad9bd-cf79-48fa-89a0-102ddf4d4e61.  SCAR - Microbial Antarctic Resource System отвечает за публикацию этого ресурса, и зарегистрирован в GBIF как издатель данных при оподдержке Scientific Committee on Antarctic Research.

Ключевые слова

Metadata

Контакты

Кто является создателем ресурса:

Igor Pessi
University of Liège Alle ́e du Six Aouˆt 13, B6a 4000 Liège BE
Yannick Lara
University of Liège Alle ́e du Six Aouˆt 13, B6a 4000 Liège BE
Benoit Durieu
University of Liège Alle ́e du Six Aouˆt 13, B6a 4000 Liège BE
Pedro de C. Maarouf
University of Liège Alle ́e du Six Aouˆt 13, B6a 4000 Liège BE
Elie Verleyen
Ghent University Krijgslaan 281 9000 Ghent BE
Annick Wilmotte
University of Liège Alle ́e du Six Aouˆt 13, B6a 4000 Liège BE

Кто может ответить на вопросы о ресурсе:

Igor Pessi
University of Liège Alle ́e du Six Aouˆt 13, B6a 4000 Liège BE

Кем заполнены метаданные:

Maxime Sweetlove
Research assistent
Royal Belgian Institute for Natural Sciences Rue Vautier 29 1000 Brussels BE

Кто еще связан с данным ресурсом:

User

Географический охват

Circum-Antarctic sampling of benthic microbial mats in lakes (n=13)

Ограничивающие координаты Юг Запад [-82.45, -67.233], Север Восток [-66.283, 100.233]

Таксономический охват

Cyanobacteria (16S ssu rRNA gene)

Phylum  Cyanobacteria (Cyanobacteria)

Временной охват

Период формирования 1997-2007

Данные проекта

CCAMBIO (Climate Change and Antarctic Microbial Biodiversity) is an academic project funded by the Belgian Federal Science Policy (BELSPO). Its main objective is to study the diversity, biogeographic zoning and genomic make-up of lacustrine microbial mat communities in the Antarctic Realm. CCAMBIO is composed by researchers from four Belgian Universities and Institutes (University of Liège, Ghent University, National Botanical Garden of Belgium and Royal Belgian Institute of Natural Sciences), as well as collaborators from the British Antarctic Survey.

Название Climate Change and Antarctic Microbial Biodiversity
Идентификатор CCAMBIO
Финансирование Belgian Science Policy Office (BelSPO) project SD/BA/03
Описание района исследования Microbial mats in the benthic and littoral zon of lakes in polar environments.
Описание плана выполнения исследований Lakes from different regions in Antarctica were sampled, and sequencing was preformed of the 16S marker genes to provide a base-line inventory of microbial eukaryotes biodiversity and test hypotheses about biogeography and species distributions

Исполнители проекта:

Igor Pessi

Методы сбора

Microbial mat samples were collected in the littoral or deeper parts of the euphotic zone of the lakes using a spatula or gravity corer, respectively. The upper 1 cm of the core was aseptically removed and kept dark and cool until transfer to -20°C.

Охват исследования Samples were taken from benthic microbial mats (upper 1 cm), collected in 13 lakes on the Antarctic continent, distributed across eight Antarctic regions belonging to four distinct Antarctic Conservation Biogeographical Regions (ACBR).
Контроль качества DNA concentration and quality were determined using a NanoVue spectrophotometer (GE Healthcare Life Sciences, Little Chalfont, UK). A blank DNA extraction consisting of sterile Milli-Q water was carried out in parallel.

Описание этапа методики:

  1. DNA was extracted from the mats using the PowerSoil DNA Isolation Kit (MOBIO Labora- tories, Carlsbad, CA, USA) according to the manufacturer’s instructions with some modifications. Tubes were agitated on a vortex for 20 extra min to ensure a good disintegration of the mats and, if not completely disintegrated, a sterile pestle was used to crush the remaining pieces.
  2. The cyanobacteria-specific primer set CYA359F and CYA781R(a)/CYA781R(b) was used to amplify the V3-V4 variable region of the 16S rRNA gene. PCR reactions consisted of 19 PCR buffer with 1.5 mM MgCl2, 1mg mL 1BSA, 200 uM of each dNTP, 0.2 uM of each primer, 1 U SUPER TAQ plus DNA polymerase (HT Biotechnology, Cambridge, UK), and 4 ng uL^-1 template DNA in a final volume of 50 uL. Amplification was performed using an initial denaturation step at 94°C for 2 min, followed by 30 cycles of 94°C for 45 s, 60°C (for primer 781Ra) or 57°C (for primer 781Rb) for 45 s and 68°C for 45 s, and a final elonga- tion at 68°C for 5 min. Negative controls (PCR mixes with either no DNA or the blank DNA extracts) were always included during PCR amplifications. To minimize stochastic PCR bias, amplification was carried out as six independent PCR reactions (three for each reverse primer) that were pooled before purification.
  3. Replicate PCR reactions were pooled and purified using the GeneJet PCR Purification Kit (Thermo Scientific, Wal- tham, MA, USA). Purified amplicons were quantified using the Quant-iT PicoGreen dsDNA Assay Kit, pooled in equimolar concentrations, and concentrated to 25 uL using the Ami- con Ultra-0.5 mL 30K device (EMD Millipore, Billerica, MA, USA). Pooled libraries were sent to Beckman Coulter Geno- mics (Takeley, UK), where primer dimers were removed using the Agencourt AMPure XP Kit (Beckman Coulter, Brea, CA, USA) and sequencing adapters were ligated to the ampli- cons. Sequences were obtained using the 454 GS FLX+ Titanium platform (454 Life Sciences, Branford, CT, USA).

Библиографические ссылки

  1. Pessi, I. S., Maalouf, P. D. C., Laughinghouse IV, H. D., Baurain, D., & Wilmotte, A. (2016). On the use of high‐throughput sequencing for the study of cyanobacterial diversity in Antarctic aquatic mats. Journal of phycology, 52(3), 356-368.
  2. Pessi, I. S., Lara, Y., Durieu, B., Maalouf, P. D. C., Verleyen, E., & Wilmotte, A. (2018). Community structure and distribution of benthic cyanobacteria in Antarctic lacustrine microbial mats. FEMS microbiology ecology, 94(5), fiy042.

Дополнительные метаданные

Альтернативные идентификаторы a41ad9bd-cf79-48fa-89a0-102ddf4d4e61
https://ipt.biodiversity.aq/resource?r=lacustrine_cyanobacteria_antarctica